Except that all the droids were probably melted down or something after Sidious deactivates them. I mean, you don't have billions of Battle Droids running around in the OT...

You have a few.

There's even stories of old battle droids attacking New Republic people according to the EU. Why would they bother going after billions of droids to melt them down... into what? More droids? Was there a big metal shortage after the war?

I guess we've figured out the great mystery after all! The reason the Death Star took so long if they were busy recycling those droid bodies... TO MAKE THE ARMOR!

Death Star = quadrillions of mooshed together droids!

Honestly though, the ones that weren't destroyed in combat would be perfectly usable. They could be used as labor or sold to raise money. They needn't have destroyed every single one of them. Seems rather like a waste.

The Empire is the Republic, so they could have never fought. Thats why I picked CIS vs Rebels. But a Empire vs. the Republic battle I would love to see.

Who cares if it never happened? 99% of the stuff in SWBF never happened and never could happen if the movies are canon! It's a game, let us have our fantasies.

Maybe the Empire wanted to see how far they'd come, so they took a bunch of Republic stuff out of mothballs, trained some decent troops according to the old stuff, and put them against each other. Boom!

Or how about this, a mischevious Time Traveler sucked a huge army from the Republic Era and inserted them ("man worlds" theory here so it's not like this destroys the Empire's creation) into a situation where they would be fighting the Empire. The Empire might realize that these are their own people from the past, but they have no time to think, the battle is on! The Republic has no idea who these similar looking guys are, but they attack! Boom!